Indeed, I was referring to preprocessed MGH data.
Cheers
Stam
> On 12 Mar 2016, at 18:17, Harms, Michael <[log in to unmask]> wrote:
>
>
> I’m guessing from the “mgh” in the file name that this is data from the
> MGH HPC, not the WU-MN HCP.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> -----------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO 63110Email: [log in to unmask]
>
>
>
>
> On 3/12/16, 9:26 AM, "FSL - FMRIB's Software Library on behalf of
> Stamatios Sotiropoulos" <[log in to unmask] on behalf of
> [log in to unmask]> wrote:
>
> I do not have that exact preprocessed version of that subject, but in the
> first version of preprocessed data I cannot see any problem.
>
> Have you looked at the data to make sure that they look fine at the
> problematic region? By the way, I don’t think that this is related, but if
> you use FSL 5.0, this is ~4 years old, you should update to 5.09.
>
> Cheers
> Stam
>
>
>
>
> On 12 Mar 2016, at 12:46, Verena Rozanski
> <[log in to unmask]> wrote:
>
>> Dear Stam,
>>
>> thank you for your answer!
>>
>> I used the following datasets:
>>
>>
>> HCP_mgh_1031_MR_ep2d_Diffusion_Gradwarped,_Eddy_Current_Corrected_Br_20141
>> 002144129918_S227836_I445964.nii.gz (renamed to „data.nii.gz“)
>> mgh_1031_bvals_ep2d_eddy.txt (renamed to „bvals“)
>> mgh_1031_bvecs_fsl_moco_norm_ep2d_eddy.txt (renamed to „bvecs“)
>>
>> and created a folder named dtifit. There, I ran the dtifit command with
>> FSL 5.0 (/usr/share/fsl/5.0/bin/dtifit --data= mgh_1031/dtifit/data
>> --out=mgh_1031/dtifit/dti --mask= mgh_1031/dtifit/nodif_brain_mask
>> --bvecs=mgh_1031/dtifit/bvecs --bvals=mgh_1031/dtifit/bvals) and studies
>> the outcome.
>>
>> Thank you,
>> best,
>>
>> Verena
>
>
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